8A49 | pdb_00008a49

Endoglycosidase S in complex with IgG1 Fc

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EN3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294.15	0.09 M halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M buffer system 2 (Sodium HEPES; MOPS (acid)), pH 7.5, 37.5 % v/v precipitant mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350) - condition B8 from Morpheus crystallisation screen (Molecular Dimensions)

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.529	α = 90
b = 174.294	β = 90
c = 193.059	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 XE 16M		2022-05-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	3.45	49.78	100	0.144	0.15	0.04	1	11.2	13.7		43678

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.45	3.51	100		1.951	2.023	0.532	0.599	0.6	14.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6EN3	3.45	49.78	43613	2116	99.954	0.255	0.2525	0.26	0.3112	0.32	146.604

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
2.654			2.667		-5.322

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	10.047
r_dihedral_angle_3_deg	9.905
r_lrange_it	8.76
r_lrange_other	8.76
r_mcangle_it	5.593
r_mcangle_other	5.593
r_dihedral_angle_1_deg	4.912
r_scangle_it	4.388
r_scangle_other	4.388
r_mcbond_it	3.217
r_mcbond_other	3.217
r_scbond_it	2.402
r_scbond_other	2.402
r_dihedral_angle_2_deg	2.107
r_angle_refined_deg	0.604
r_angle_other_deg	0.234
r_symmetry_xyhbond_nbd_refined	0.179
r_symmetry_nbd_refined	0.167
r_nbtor_refined	0.165
r_symmetry_nbd_other	0.161
r_nbd_refined	0.159
r_nbd_other	0.146
r_xyhbond_nbd_refined	0.109
r_ncsr_local_group_1	0.087
r_symmetry_nbtor_other	0.075
r_ncsr_local_group_2	0.069
r_chiral_restr	0.028
r_chiral_restr_other	0.017
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16920
Nucleic Acid Atoms
Solvent Atoms	68
Heterogen Atoms	99

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
MOLREP	phasing